Starting phenix.real_space_refine
on Tue Mar 11 20:22:01 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/9bap_44410/03_2025/9bap_44410.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bap_44410/03_2025/9bap_44410.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.88
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bap_44410/03_2025/9bap_44410.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bap_44410/03_2025/9bap_44410.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bap_44410/03_2025/9bap_44410.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bap_44410/03_2025/9bap_44410.cif"
  }
  resolution = 2.88
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.029
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      26      5.16       5
     C    4198      2.51       5
     N    1157      2.21       5
     O    1153      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6535
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 6508
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 886, 6508
          Classifications: {'peptide': 886}
          Incomplete info: {'truncation_to_alanine': 157}
          Link IDs: {'PTRANS': 58, 'TRANS': 827}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 627
          Unresolved non-hydrogen angles: 761
          Unresolved non-hydrogen dihedrals: 527
          Unresolved non-hydrogen chiralities: 22
          Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 3, 'TYR:plan': 8, 'ASN:plan1': 10, 'ASP:plan': 15, 'PHE:plan': 2, 'GLU:plan': 26, 'ARG:plan': 17}
          Unresolved non-hydrogen planarities: 387
    Chain: "A"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 26
          Classifications: {'peptide': 1}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2506  SG  CYS A 635      30.352  43.644  28.469  1.00133.87           S
  ATOM   2519  SG  CYS A 637      31.148  42.910  25.866  1.00128.15           S
  ATOM   2923  SG  CYS A 692      33.962  42.961  27.064  1.00122.87           S

  Time building chain proxies: 4.14, per 1000 atoms: 0.63
  Number of scatterers: 6535
  At special positions: 0
  Unit cell: (66.34, 93.09, 146.59, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      26     16.00
     O    1153      8.00
     N    1157      7.00
     C    4198      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.52
  Conformation dependent library (CDL) restraints added in 995.8 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1502 "
        pdb="ZN    ZN A1502 " - pdb=" SG  CYS A 637 "
        pdb="ZN    ZN A1502 " - pdb=" SG  CYS A 692 "
        pdb="ZN    ZN A1502 " - pdb=" SG  CYS A 635 "
        pdb="ZN    ZN A1502 " - pdb=" ND1 HIS A 694 "
      Number of angles added : 3


  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1636

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 11 sheets defined
      28.1% alpha, 27.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.96
  Creating SS restraints...
    Processing helix  chain 'A' and resid 163 through 179
      removed outlier: 4.162A  pdb=" N   ALA A 167 " --> pdb=" O   PRO A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 213
      removed outlier: 3.775A  pdb=" N   VAL A 212 " --> pdb=" O   PRO A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 311
      Proline residue:  A 289  - end of helix
      removed outlier: 3.902A  pdb=" N   TRP A 292 " --> pdb=" O   GLN A 288 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   VAL A 301 " --> pdb=" O   GLY A 297 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   ASP A 302 " --> pdb=" O   LYS A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 322
      removed outlier: 4.572A  pdb=" N   SER A 321 " --> pdb=" O   GLY A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 329
    Processing helix  chain 'A' and resid 334 through 343
      removed outlier: 3.987A  pdb=" N   GLN A 343 " --> pdb=" O   ASN A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 356
      removed outlier: 3.584A  pdb=" N   ASN A 356 " --> pdb=" O   SER A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 366
    Processing helix  chain 'A' and resid 371 through 375
    Processing helix  chain 'A' and resid 376 through 381
      removed outlier: 3.865A  pdb=" N   ARG A 380 " --> pdb=" O   ASP A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
    Processing helix  chain 'A' and resid 425 through 429
      removed outlier: 4.192A  pdb=" N   VAL A 429 " --> pdb=" O   ILE A 425 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 425 through 429'
    Processing helix  chain 'A' and resid 547 through 551
    Processing helix  chain 'A' and resid 640 through 644
      removed outlier: 3.754A  pdb=" N   ALA A 643 " --> pdb=" O   GLY A 640 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 690
      removed outlier: 3.992A  pdb=" N   LEU A 690 " --> pdb=" O   LYS A 687 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 850 through 860
    Processing helix  chain 'A' and resid 871 through 882
    Processing helix  chain 'A' and resid 894 through 904
      removed outlier: 3.501A  pdb=" N   LEU A 898 " --> pdb=" O   SER A 894 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 938 through 959
      removed outlier: 3.551A  pdb=" N   VAL A 942 " --> pdb=" O   VAL A 938 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   VAL A 948 " --> pdb=" O   ASN A 944 " (cutoff:3.500A)
      removed outlier: 4.489A  pdb=" N   ALA A 949 " --> pdb=" O   GLN A 945 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 981 through 993
    Processing helix  chain 'A' and resid 1005 through 1008
      removed outlier: 3.707A  pdb=" N   GLY A1008 " --> pdb=" O   TRP A1005 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1005 through 1008'
    Processing helix  chain 'A' and resid 1068 through 1073
    Processing helix  chain 'A' and resid 1189 through 1197
    Processing helix  chain 'A' and resid 1208 through 1218
    Processing helix  chain 'A' and resid 1221 through 1237
    Processing sheet with id=AA1, first strand: chain 'A' and resid 205 through 206
      removed outlier: 3.611A  pdb=" N   GLU A 205 " --> pdb=" O   VAL A 197 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   VAL A 197 " --> pdb=" O   GLU A 205 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   TYR A 273 " --> pdb=" O   ILE A 186 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   PHE A 188 " --> pdb=" O   TYR A 273 " (cutoff:3.500A)
      removed outlier: 7.622A  pdb=" N   ASP A 192 " --> pdb=" O   LYS A 277 " (cutoff:3.500A)
      removed outlier: 7.622A  pdb=" N   ASN A 194 " --> pdb=" O   PRO A 279 " (cutoff:3.500A)
      removed outlier: 7.346A  pdb=" N   ILE A 272 " --> pdb=" O   SER A 264 " (cutoff:3.500A)
      removed outlier: 4.400A  pdb=" N   SER A 264 " --> pdb=" O   ILE A 272 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   GLU A 243 " --> pdb=" O   ARG A 263 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   GLY A 238 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   PHE A 223 " --> pdb=" O   GLY A 238 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   VAL A 226 " --> pdb=" O   ASP A 192 " (cutoff:3.500A)
      removed outlier: 5.722A  pdb=" N   ASP A 192 " --> pdb=" O   VAL A 226 " (cutoff:3.500A)
      removed outlier: 6.990A  pdb=" N   LYS A 228 " --> pdb=" O   LEU A 190 " (cutoff:3.500A)
      removed outlier: 5.556A  pdb=" N   LEU A 190 " --> pdb=" O   LYS A 228 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 400 through 402
    Processing sheet with id=AA3, first strand: chain 'A' and resid 411 through 412
      removed outlier: 5.385A  pdb=" N   THR A 411 " --> pdb=" O   ARG A 431 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 556 through 559
      removed outlier: 5.254A  pdb=" N   PHE A 582 " --> pdb=" O   PHE A 610 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   ASP A 606 " --> pdb=" O   GLN A 586 " (cutoff:3.500A)
      removed outlier: 4.737A  pdb=" N   VAL A 588 " --> pdb=" O   SER A 604 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   SER A 604 " --> pdb=" O   VAL A 588 " (cutoff:3.500A)
      removed outlier: 7.280A  pdb=" N   VAL A 607 " --> pdb=" O   HIS A 634 " (cutoff:3.500A)
      removed outlier: 7.418A  pdb=" N   HIS A 634 " --> pdb=" O   VAL A 607 " (cutoff:3.500A)
      removed outlier: 5.402A  pdb=" N   TRP A 609 " --> pdb=" O   SER A 632 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 556 through 559
      removed outlier: 5.254A  pdb=" N   PHE A 582 " --> pdb=" O   PHE A 610 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   ASP A 606 " --> pdb=" O   GLN A 586 " (cutoff:3.500A)
      removed outlier: 4.737A  pdb=" N   VAL A 588 " --> pdb=" O   SER A 604 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   SER A 604 " --> pdb=" O   VAL A 588 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 656 through 658
    Processing sheet with id=AA7, first strand: chain 'A' and resid 673 through 676
    Processing sheet with id=AA8, first strand: chain 'A' and resid 776 through 779
      removed outlier: 3.636A  pdb=" N   GLY A 778 " --> pdb=" O   LEU A 712 " (cutoff:3.500A)
      removed outlier: 12.424A  pdb=" N   ASP A 723 " --> pdb=" O   ARG A 748 " (cutoff:3.500A)
      removed outlier: 10.025A  pdb=" N   ARG A 748 " --> pdb=" O   ASP A 723 " (cutoff:3.500A)
      removed outlier: 6.122A  pdb=" N   TYR A 725 " --> pdb=" O   LEU A 746 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   LEU A 746 " --> pdb=" O   TYR A 725 " (cutoff:3.500A)
      removed outlier: 5.736A  pdb=" N   VAL A 727 " --> pdb=" O   ARG A 744 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   ARG A 744 " --> pdb=" O   VAL A 727 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   GLU A 729 " --> pdb=" O   ARG A 742 " (cutoff:3.500A)
      removed outlier: 5.014A  pdb=" N   ASP A 767 " --> pdb=" O   LYS A 745 " (cutoff:3.500A)
      removed outlier: 7.409A  pdb=" N   LEU A 747 " --> pdb=" O   THR A 765 " (cutoff:3.500A)
      removed outlier: 7.051A  pdb=" N   THR A 765 " --> pdb=" O   LEU A 747 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   LEU A 762 " --> pdb=" O   HIS A 808 " (cutoff:3.500A)
      removed outlier: 7.950A  pdb=" N   GLN A 810 " --> pdb=" O   LEU A 762 " (cutoff:3.500A)
      removed outlier: 7.114A  pdb=" N   TYR A 764 " --> pdb=" O   GLN A 810 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   ILE A 781 " --> pdb=" O   PHE A 804 " (cutoff:3.500A)
      removed outlier: 7.872A  pdb=" N   ILE A 806 " --> pdb=" O   ILE A 781 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   ARG A 783 " --> pdb=" O   ILE A 806 " (cutoff:3.500A)
      removed outlier: 8.959A  pdb=" N   HIS A 808 " --> pdb=" O   ARG A 783 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 776 through 779
      removed outlier: 3.636A  pdb=" N   GLY A 778 " --> pdb=" O   LEU A 712 " (cutoff:3.500A)
      removed outlier: 12.424A  pdb=" N   ASP A 723 " --> pdb=" O   ARG A 748 " (cutoff:3.500A)
      removed outlier: 10.025A  pdb=" N   ARG A 748 " --> pdb=" O   ASP A 723 " (cutoff:3.500A)
      removed outlier: 6.122A  pdb=" N   TYR A 725 " --> pdb=" O   LEU A 746 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   LEU A 746 " --> pdb=" O   TYR A 725 " (cutoff:3.500A)
      removed outlier: 5.736A  pdb=" N   VAL A 727 " --> pdb=" O   ARG A 744 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   ARG A 744 " --> pdb=" O   VAL A 727 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   GLU A 729 " --> pdb=" O   ARG A 742 " (cutoff:3.500A)
      removed outlier: 5.014A  pdb=" N   ASP A 767 " --> pdb=" O   LYS A 745 " (cutoff:3.500A)
      removed outlier: 7.409A  pdb=" N   LEU A 747 " --> pdb=" O   THR A 765 " (cutoff:3.500A)
      removed outlier: 7.051A  pdb=" N   THR A 765 " --> pdb=" O   LEU A 747 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   LEU A 762 " --> pdb=" O   HIS A 808 " (cutoff:3.500A)
      removed outlier: 7.950A  pdb=" N   GLN A 810 " --> pdb=" O   LEU A 762 " (cutoff:3.500A)
      removed outlier: 7.114A  pdb=" N   TYR A 764 " --> pdb=" O   GLN A 810 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 891 through 892
      removed outlier: 3.693A  pdb=" N   ASP A 869 " --> pdb=" O   PHE A 891 " (cutoff:3.500A)
      removed outlier: 5.686A  pdb=" N   LEU A 840 " --> pdb=" O   GLU A 863 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   ARG A 865 " --> pdb=" O   LEU A 840 " (cutoff:3.500A)
      removed outlier: 7.897A  pdb=" N   GLY A 842 " --> pdb=" O   ARG A 865 " (cutoff:3.500A)
      removed outlier: 6.126A  pdb=" N   ALA A 867 " --> pdb=" O   GLY A 842 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   ASP A 844 " --> pdb=" O   ALA A 867 " (cutoff:3.500A)
      removed outlier: 5.816A  pdb=" N   ASP A 869 " --> pdb=" O   ASP A 844 " (cutoff:3.500A)
      removed outlier: 5.777A  pdb=" N   ARG A 841 " --> pdb=" O   PHE A 919 " (cutoff:3.500A)
      removed outlier: 7.377A  pdb=" N   ALA A 921 " --> pdb=" O   ARG A 841 " (cutoff:3.500A)
      removed outlier: 5.992A  pdb=" N   MET A 843 " --> pdb=" O   ALA A 921 " (cutoff:3.500A)
      removed outlier: 6.381A  pdb=" N   ILE A 920 " --> pdb=" O   VAL A 964 " (cutoff:3.500A)
      removed outlier: 8.030A  pdb=" N   GLU A 966 " --> pdb=" O   ILE A 920 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   ALA A 922 " --> pdb=" O   GLU A 966 " (cutoff:3.500A)
      removed outlier: 8.962A  pdb=" N   VAL A 968 " --> pdb=" O   ALA A 922 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1044 through 1045

    230 hydrogen bonds defined for protein.
    627 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.43

  Time building geometry restraints manager: 1.81 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.22 -     1.34: 2162
        1.34 -     1.46: 1655
        1.46 -     1.58: 2868
        1.58 -     1.70: 0
        1.70 -     1.82: 36
  Bond restraints: 6721
  Sorted by residual:
  bond pdb=" N   PHE A 391 "
       pdb=" CA  PHE A 391 "
    ideal  model  delta    sigma   weight residual
    1.455  1.490 -0.035 1.23e-02 6.61e+03 8.03e+00
  bond pdb=" N   GLN A 393 "
       pdb=" CA  GLN A 393 "
    ideal  model  delta    sigma   weight residual
    1.456  1.485 -0.029 1.29e-02 6.01e+03 4.95e+00
  bond pdb=" N   ARG A 392 "
       pdb=" CA  ARG A 392 "
    ideal  model  delta    sigma   weight residual
    1.454  1.481 -0.027 1.32e-02 5.74e+03 4.04e+00
  bond pdb=" N   GLU A 394 "
       pdb=" CA  GLU A 394 "
    ideal  model  delta    sigma   weight residual
    1.462  1.483 -0.021 1.31e-02 5.83e+03 2.55e+00
  bond pdb=" CB  VAL A 982 "
       pdb=" CG1 VAL A 982 "
    ideal  model  delta    sigma   weight residual
    1.521  1.481  0.040 3.30e-02 9.18e+02 1.49e+00
  ... (remaining 6716 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.10: 9062
        2.10 -     4.20: 118
        4.20 -     6.29: 14
        6.29 -     8.39: 1
        8.39 -    10.49: 3
  Bond angle restraints: 9198
  Sorted by residual:
  angle pdb=" C   CYS A 619 "
        pdb=" CA  CYS A 619 "
        pdb=" CB  CYS A 619 "
      ideal   model   delta    sigma   weight residual
     115.79  110.20    5.59 1.19e+00 7.06e-01 2.21e+01
  angle pdb=" CB  MET A1193 "
        pdb=" CG  MET A1193 "
        pdb=" SD  MET A1193 "
      ideal   model   delta    sigma   weight residual
     112.70  123.19  -10.49 3.00e+00 1.11e-01 1.22e+01
  angle pdb=" CA  ARG A 392 "
        pdb=" C   ARG A 392 "
        pdb=" O   ARG A 392 "
      ideal   model   delta    sigma   weight residual
     121.87  118.38    3.49 1.10e+00 8.26e-01 1.01e+01
  angle pdb=" N   GLU A 394 "
        pdb=" CA  GLU A 394 "
        pdb=" C   GLU A 394 "
      ideal   model   delta    sigma   weight residual
     112.72  108.48    4.24 1.36e+00 5.41e-01 9.70e+00
  angle pdb=" CA  TYR A 416 "
        pdb=" CB  TYR A 416 "
        pdb=" CG  TYR A 416 "
      ideal   model   delta    sigma   weight residual
     113.90  119.33   -5.43 1.80e+00 3.09e-01 9.10e+00
  ... (remaining 9193 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.08: 3371
       16.08 -    32.15: 362
       32.15 -    48.23: 119
       48.23 -    64.30: 30
       64.30 -    80.38: 6
  Dihedral angle restraints: 3888
    sinusoidal: 1341
      harmonic: 2547
  Sorted by residual:
  dihedral pdb=" CA  LYS A1083 "
           pdb=" C   LYS A1083 "
           pdb=" N   PRO A1084 "
           pdb=" CA  PRO A1084 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.84   17.16     0      5.00e+00 4.00e-02 1.18e+01
  dihedral pdb=" CA  TRP A1153 "
           pdb=" CB  TRP A1153 "
           pdb=" CG  TRP A1153 "
           pdb=" CD1 TRP A1153 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  159.15  -69.15     2      2.00e+01 2.50e-03 1.05e+01
  dihedral pdb=" CA  ASP A 884 "
           pdb=" CB  ASP A 884 "
           pdb=" CG  ASP A 884 "
           pdb=" OD1 ASP A 884 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -83.51   53.51     1      2.00e+01 2.50e-03 9.73e+00
  ... (remaining 3885 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 650
       0.031 -    0.063: 242
       0.063 -    0.094: 68
       0.094 -    0.125: 50
       0.125 -    0.156: 7
  Chirality restraints: 1017
  Sorted by residual:
  chirality pdb=" CA  ARG A 392 "
            pdb=" N   ARG A 392 "
            pdb=" C   ARG A 392 "
            pdb=" CB  ARG A 392 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.10e-01
  chirality pdb=" CG  LEU A 986 "
            pdb=" CB  LEU A 986 "
            pdb=" CD1 LEU A 986 "
            pdb=" CD2 LEU A 986 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.45   -0.14 2.00e-01 2.50e+01 4.92e-01
  chirality pdb=" CA  PHE A 659 "
            pdb=" N   PHE A 659 "
            pdb=" C   PHE A 659 "
            pdb=" CB  PHE A 659 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.73e-01
  ... (remaining 1014 not shown)

  Planarity restraints: 1205
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 889 "   -0.038 5.00e-02 4.00e+02   5.75e-02 5.29e+00
        pdb=" N   PRO A 890 "    0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO A 890 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 890 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 882 "   -0.024 5.00e-02 4.00e+02   3.71e-02 2.20e+00
        pdb=" N   PRO A 883 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO A 883 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 883 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 716 "    0.024 5.00e-02 4.00e+02   3.59e-02 2.06e+00
        pdb=" N   PRO A 717 "   -0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO A 717 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 717 "    0.020 5.00e-02 4.00e+02
  ... (remaining 1202 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 187
        2.71 -     3.26: 6270
        3.26 -     3.80: 10300
        3.80 -     4.35: 12699
        4.35 -     4.90: 21552
  Nonbonded interactions: 51008
  Sorted by model distance:
  nonbonded pdb=" O   TYR A 229 "
            pdb=" OG1 THR A 232 "
     model   vdw
     2.159 3.040
  nonbonded pdb=" OH  TYR A 303 "
            pdb=" OD2 ASP A 322 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" N   GLU A 904 "
            pdb=" OE1 GLU A 904 "
     model   vdw
     2.272 3.120
  nonbonded pdb=" NH2 ARG A 748 "
            pdb=" O   ALA A1063 "
     model   vdw
     2.275 3.120
  nonbonded pdb=" O   PRO A 912 "
            pdb=" OH  TYR A 958 "
     model   vdw
     2.288 3.040
  ... (remaining 51003 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.730
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     20.510
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6565
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6721  Z= 0.212
  Angle     :  0.582  10.491   9198  Z= 0.295
  Chirality :  0.042   0.156   1017
  Planarity :  0.005   0.057   1205
  Dihedral  : 15.770  80.379   2252
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  : 32.21 %
    Favored  : 66.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.28), residues: 874
  helix: -0.06 (0.36), residues: 210
  sheet: -0.55 (0.38), residues: 169
  loop : -0.05 (0.28), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1005 
 HIS   0.003   0.000   HIS A 299 
 PHE   0.013   0.001   PHE A1090 
 TYR   0.015   0.001   TYR A1019 
 ARG   0.004   0.000   ARG A 431 

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 84
  time to evaluate  : 0.647 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  287 TYR cc_start: 0.7630 (t80) cc_final: 0.7386 (t80)
REVERT: A  871 TRP cc_start: 0.6053 (t60) cc_final: 0.5375 (t60)
REVERT: A  879 MET cc_start: 0.6759 (mmm) cc_final: 0.6270 (mmm)
  outliers start: 5
  outliers final: 5
  residues processed: 89
  average time/residue: 0.8699
  time to fit residues: 83.4516
Evaluate side-chains
  72 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  391 PHE
Chi-restraints excluded: chain A residue  917 VAL
Chi-restraints excluded: chain A residue 1161 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   chunk 37 optimal weight:    3.9990
   chunk 22 optimal weight:    0.7980
   chunk 44 optimal weight:    5.9990
   chunk 35 optimal weight:    7.9990
   chunk 68 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 41 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9990
   chunk 79 optimal weight:    1.9990
   overall best weight:    1.1386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 356 ASN
A 393 GLN
** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 876 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.170609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.142257 restraints weight = 8772.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.3867 rms_B_bonded: 2.97
r_work: 0.3751 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6712
moved from start:          0.1037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6721  Z= 0.290
  Angle     :  0.611   7.952   9198  Z= 0.313
  Chirality :  0.043   0.142   1017
  Planarity :  0.005   0.039   1205
  Dihedral  :  5.109  47.392    963
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  6.38 %
    Allowed  : 26.17 %
    Favored  : 67.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.28), residues: 874
  helix: -0.10 (0.35), residues: 219
  sheet: -0.67 (0.39), residues: 167
  loop : -0.12 (0.29), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A1005 
 HIS   0.007   0.001   HIS A 299 
 PHE   0.036   0.002   PHE A 659 
 TYR   0.022   0.002   TYR A1019 
 ARG   0.006   0.001   ARG A 392 

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 65
  time to evaluate  : 0.712 
Fit side-chains
REVERT: A  211 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6850 (pp)
REVERT: A  263 ARG cc_start: 0.6027 (mmt90) cc_final: 0.5747 (mmt90)
REVERT: A  338 GLN cc_start: 0.6797 (mm-40) cc_final: 0.6524 (mp-120)
REVERT: A  761 GLU cc_start: 0.7646 (tp30) cc_final: 0.7415 (tp30)
REVERT: A  879 MET cc_start: 0.6762 (mmm) cc_final: 0.6319 (mmm)
REVERT: A  888 THR cc_start: 0.8112 (m) cc_final: 0.7857 (t)
REVERT: A  981 ASP cc_start: 0.6340 (OUTLIER) cc_final: 0.6061 (m-30)
REVERT: A 1192 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.6539 (mm-30)
REVERT: A 1203 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6854 (mt-10)
  outliers start: 38
  outliers final: 16
  residues processed: 97
  average time/residue: 0.7751
  time to fit residues: 81.4451
Evaluate side-chains
  85 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 65
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  391 PHE
Chi-restraints excluded: chain A residue  585 VAL
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  661 THR
Chi-restraints excluded: chain A residue  683 ILE
Chi-restraints excluded: chain A residue  716 SER
Chi-restraints excluded: chain A residue  784 CYS
Chi-restraints excluded: chain A residue  895 VAL
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  917 VAL
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue  981 ASP
Chi-restraints excluded: chain A residue 1092 ASP
Chi-restraints excluded: chain A residue 1161 LEU
Chi-restraints excluded: chain A residue 1168 THR
Chi-restraints excluded: chain A residue 1192 GLU
Chi-restraints excluded: chain A residue 1203 GLU
Chi-restraints excluded: chain A residue 1222 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 2 optimal weight:    0.0270
   chunk 30 optimal weight:    7.9990
   chunk 49 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 82 optimal weight:    0.0270
   chunk 77 optimal weight:    0.0170
   chunk 78 optimal weight:    0.9980
   chunk 68 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   overall best weight:    0.3334

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 356 ASN
A 393 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.174245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.146365 restraints weight = 8827.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.3923 rms_B_bonded: 3.00
r_work: 0.3811 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6539
moved from start:          0.1096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6721  Z= 0.166
  Angle     :  0.543   8.395   9198  Z= 0.271
  Chirality :  0.041   0.139   1017
  Planarity :  0.004   0.042   1205
  Dihedral  :  4.809  46.278    962
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  5.70 %
    Allowed  : 26.68 %
    Favored  : 67.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.29), residues: 874
  helix:  0.28 (0.35), residues: 222
  sheet: -0.67 (0.39), residues: 167
  loop : -0.02 (0.29), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 658 
 HIS   0.003   0.001   HIS A 299 
 PHE   0.024   0.001   PHE A 659 
 TYR   0.023   0.002   TYR A1019 
 ARG   0.003   0.000   ARG A 392 

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 78
  time to evaluate  : 0.638 
Fit side-chains
   revert: symmetry clash
REVERT: A  239 MET cc_start: 0.5272 (OUTLIER) cc_final: 0.4646 (ppp)
REVERT: A  263 ARG cc_start: 0.5832 (mmt90) cc_final: 0.5555 (mmt90)
REVERT: A  334 SER cc_start: 0.8491 (t) cc_final: 0.7295 (p)
REVERT: A  338 GLN cc_start: 0.6641 (mm-40) cc_final: 0.6338 (mp10)
REVERT: A  416 TYR cc_start: 0.6086 (t80) cc_final: 0.5884 (t80)
REVERT: A  580 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7421 (ptt90)
REVERT: A  879 MET cc_start: 0.6663 (mmm) cc_final: 0.6152 (mmm)
REVERT: A  888 THR cc_start: 0.7891 (m) cc_final: 0.7551 (t)
REVERT: A  981 ASP cc_start: 0.6202 (OUTLIER) cc_final: 0.5959 (m-30)
REVERT: A 1192 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.6369 (mm-30)
REVERT: A 1203 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6797 (mt-10)
  outliers start: 34
  outliers final: 12
  residues processed: 108
  average time/residue: 0.8562
  time to fit residues: 99.1549
Evaluate side-chains
  84 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 67
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  239 MET
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  391 PHE
Chi-restraints excluded: chain A residue  557 ILE
Chi-restraints excluded: chain A residue  580 ARG
Chi-restraints excluded: chain A residue  716 SER
Chi-restraints excluded: chain A residue  728 VAL
Chi-restraints excluded: chain A residue  846 TYR
Chi-restraints excluded: chain A residue  917 VAL
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue  981 ASP
Chi-restraints excluded: chain A residue 1161 LEU
Chi-restraints excluded: chain A residue 1168 THR
Chi-restraints excluded: chain A residue 1192 GLU
Chi-restraints excluded: chain A residue 1203 GLU
Chi-restraints excluded: chain A residue 1222 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 77 optimal weight:    0.0570
   chunk 75 optimal weight:    0.0000
   chunk 72 optimal weight:    0.5980
   chunk 30 optimal weight:    7.9990
   chunk 48 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 54 optimal weight:    0.0980
   chunk 35 optimal weight:    0.8980
   chunk 67 optimal weight:    0.5980
   chunk 62 optimal weight:    0.3980
   chunk 81 optimal weight:   10.0000
   overall best weight:    0.2302

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 356 ASN
A 393 GLN
** A 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.176195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.148413 restraints weight = 8901.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.3950 rms_B_bonded: 3.01
r_work: 0.3836 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6529
moved from start:          0.1272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   6721  Z= 0.154
  Angle     :  0.540   8.838   9198  Z= 0.264
  Chirality :  0.041   0.131   1017
  Planarity :  0.004   0.043   1205
  Dihedral  :  4.636  45.089    962
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  5.54 %
    Allowed  : 27.52 %
    Favored  : 66.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.28), residues: 874
  helix:  0.34 (0.35), residues: 222
  sheet: -0.69 (0.39), residues: 167
  loop :  0.02 (0.29), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A1005 
 HIS   0.003   0.000   HIS A 299 
 PHE   0.020   0.001   PHE A 659 
 TYR   0.018   0.001   TYR A1019 
 ARG   0.003   0.000   ARG A 786 

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 73
  time to evaluate  : 0.642 
Fit side-chains
   revert: symmetry clash
REVERT: A  239 MET cc_start: 0.5366 (OUTLIER) cc_final: 0.4776 (ppp)
REVERT: A  263 ARG cc_start: 0.5876 (mmt90) cc_final: 0.5484 (ttt90)
REVERT: A  334 SER cc_start: 0.8435 (t) cc_final: 0.7252 (p)
REVERT: A  338 GLN cc_start: 0.6740 (mm-40) cc_final: 0.6479 (mp10)
REVERT: A  580 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7419 (ptt90)
REVERT: A  871 TRP cc_start: 0.6023 (t60) cc_final: 0.5329 (t60)
REVERT: A  879 MET cc_start: 0.6695 (mmm) cc_final: 0.6259 (mmm)
REVERT: A 1192 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.6351 (mm-30)
REVERT: A 1203 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6778 (mt-10)
  outliers start: 33
  outliers final: 16
  residues processed: 101
  average time/residue: 0.8760
  time to fit residues: 95.0820
Evaluate side-chains
  93 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 73
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  239 MET
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  391 PHE
Chi-restraints excluded: chain A residue  412 ILE
Chi-restraints excluded: chain A residue  557 ILE
Chi-restraints excluded: chain A residue  580 ARG
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  661 THR
Chi-restraints excluded: chain A residue  716 SER
Chi-restraints excluded: chain A residue  728 VAL
Chi-restraints excluded: chain A residue  846 TYR
Chi-restraints excluded: chain A residue  895 VAL
Chi-restraints excluded: chain A residue  917 VAL
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue 1161 LEU
Chi-restraints excluded: chain A residue 1164 THR
Chi-restraints excluded: chain A residue 1168 THR
Chi-restraints excluded: chain A residue 1192 GLU
Chi-restraints excluded: chain A residue 1203 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 66 optimal weight:    0.2980
   chunk 27 optimal weight:    8.9990
   chunk 34 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 61 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9980
   chunk 86 optimal weight:    2.9990
   chunk 67 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 51 optimal weight:    0.7980
   chunk 44 optimal weight:    5.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 356 ASN
A 393 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.173538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.145519 restraints weight = 8909.399|
|-----------------------------------------------------------------------------|
r_work (start): 0.3906 rms_B_bonded: 2.99
r_work: 0.3791 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6577
moved from start:          0.1423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6721  Z= 0.214
  Angle     :  0.566   8.861   9198  Z= 0.280
  Chirality :  0.042   0.137   1017
  Planarity :  0.004   0.044   1205
  Dihedral  :  4.732  45.190    962
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 27.85 %
    Favored  : 67.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.28), residues: 874
  helix:  0.49 (0.36), residues: 216
  sheet: -0.68 (0.40), residues: 163
  loop :  0.02 (0.28), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 658 
 HIS   0.006   0.001   HIS A 299 
 PHE   0.018   0.002   PHE A 659 
 TYR   0.031   0.002   TYR A 287 
 ARG   0.004   0.000   ARG A 900 

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 73
  time to evaluate  : 0.667 
Fit side-chains
   revert: symmetry clash
REVERT: A  239 MET cc_start: 0.5342 (OUTLIER) cc_final: 0.4774 (ppp)
REVERT: A  334 SER cc_start: 0.8499 (t) cc_final: 0.7311 (p)
REVERT: A  338 GLN cc_start: 0.6789 (mm-40) cc_final: 0.6522 (mp10)
REVERT: A  580 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7551 (ptt90)
REVERT: A  871 TRP cc_start: 0.6048 (t60) cc_final: 0.5321 (t60)
REVERT: A  879 MET cc_start: 0.6690 (mmm) cc_final: 0.6375 (mmm)
REVERT: A 1094 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.7069 (mtm180)
REVERT: A 1192 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.6358 (mm-30)
REVERT: A 1203 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6806 (mt-10)
  outliers start: 29
  outliers final: 15
  residues processed: 98
  average time/residue: 0.8402
  time to fit residues: 88.6452
Evaluate side-chains
  90 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 70
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  239 MET
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  391 PHE
Chi-restraints excluded: chain A residue  557 ILE
Chi-restraints excluded: chain A residue  580 ARG
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  661 THR
Chi-restraints excluded: chain A residue  716 SER
Chi-restraints excluded: chain A residue  728 VAL
Chi-restraints excluded: chain A residue  895 VAL
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  917 VAL
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue 1094 ARG
Chi-restraints excluded: chain A residue 1161 LEU
Chi-restraints excluded: chain A residue 1164 THR
Chi-restraints excluded: chain A residue 1168 THR
Chi-restraints excluded: chain A residue 1192 GLU
Chi-restraints excluded: chain A residue 1203 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 61 optimal weight:    0.0170
   chunk 31 optimal weight:    0.6980
   chunk 59 optimal weight:    0.4980
   chunk 43 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 69 optimal weight:    0.3980
   chunk 80 optimal weight:    0.0980
   chunk 19 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   overall best weight:    0.3418

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 356 ASN
A 393 GLN
** A 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.174820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.146639 restraints weight = 8786.275|
|-----------------------------------------------------------------------------|
r_work (start): 0.3923 rms_B_bonded: 3.01
r_work: 0.3809 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6526
moved from start:          0.1493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6721  Z= 0.165
  Angle     :  0.546   9.050   9198  Z= 0.269
  Chirality :  0.041   0.131   1017
  Planarity :  0.004   0.045   1205
  Dihedral  :  4.617  44.571    962
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 28.52 %
    Favored  : 66.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.28), residues: 874
  helix:  0.73 (0.37), residues: 211
  sheet: -0.72 (0.39), residues: 166
  loop :  0.10 (0.28), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A1005 
 HIS   0.003   0.000   HIS A 299 
 PHE   0.016   0.001   PHE A 659 
 TYR   0.027   0.001   TYR A1019 
 ARG   0.007   0.000   ARG A 263 

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 73
  time to evaluate  : 0.668 
Fit side-chains
   revert: symmetry clash
REVERT: A  239 MET cc_start: 0.5323 (OUTLIER) cc_final: 0.4743 (ppp)
REVERT: A  263 ARG cc_start: 0.6183 (mtt90) cc_final: 0.5687 (tpp80)
REVERT: A  334 SER cc_start: 0.8484 (t) cc_final: 0.7308 (p)
REVERT: A  338 GLN cc_start: 0.6773 (mm-40) cc_final: 0.6521 (mp10)
REVERT: A  580 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7471 (ptt90)
REVERT: A 1094 ARG cc_start: 0.7306 (OUTLIER) cc_final: 0.7036 (mtm180)
REVERT: A 1192 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.6305 (mm-30)
REVERT: A 1203 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6698 (mt-10)
  outliers start: 30
  outliers final: 17
  residues processed: 96
  average time/residue: 0.8828
  time to fit residues: 91.3570
Evaluate side-chains
  94 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 72
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  239 MET
Chi-restraints excluded: chain A residue  391 PHE
Chi-restraints excluded: chain A residue  393 GLN
Chi-restraints excluded: chain A residue  557 ILE
Chi-restraints excluded: chain A residue  580 ARG
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  661 THR
Chi-restraints excluded: chain A residue  716 SER
Chi-restraints excluded: chain A residue  728 VAL
Chi-restraints excluded: chain A residue  846 TYR
Chi-restraints excluded: chain A residue  888 THR
Chi-restraints excluded: chain A residue  895 VAL
Chi-restraints excluded: chain A residue  917 VAL
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue 1000 ILE
Chi-restraints excluded: chain A residue 1094 ARG
Chi-restraints excluded: chain A residue 1161 LEU
Chi-restraints excluded: chain A residue 1164 THR
Chi-restraints excluded: chain A residue 1168 THR
Chi-restraints excluded: chain A residue 1192 GLU
Chi-restraints excluded: chain A residue 1203 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 77 optimal weight:    0.0770
   chunk 45 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 72 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9980
   chunk 43 optimal weight:    0.0770
   chunk 76 optimal weight:    0.0060
   chunk 3 optimal weight:    0.8980
   chunk 40 optimal weight:    7.9990
   overall best weight:    0.3912

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 356 ASN
A 393 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.174919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.147077 restraints weight = 8712.687|
|-----------------------------------------------------------------------------|
r_work (start): 0.3924 rms_B_bonded: 2.97
r_work: 0.3808 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6525
moved from start:          0.1537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6721  Z= 0.173
  Angle     :  0.555   9.069   9198  Z= 0.273
  Chirality :  0.041   0.134   1017
  Planarity :  0.004   0.045   1205
  Dihedral  :  4.584  44.371    961
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 28.69 %
    Favored  : 66.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.28), residues: 874
  helix:  0.73 (0.36), residues: 211
  sheet: -0.70 (0.39), residues: 166
  loop :  0.11 (0.28), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 292 
 HIS   0.004   0.000   HIS A 299 
 PHE   0.015   0.001   PHE A 659 
 TYR   0.020   0.001   TYR A1019 
 ARG   0.007   0.000   ARG A 263 

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 74
  time to evaluate  : 0.669 
Fit side-chains
   revert: symmetry clash
REVERT: A  239 MET cc_start: 0.5337 (OUTLIER) cc_final: 0.4757 (ppp)
REVERT: A  334 SER cc_start: 0.8481 (t) cc_final: 0.7437 (p)
REVERT: A  338 GLN cc_start: 0.6768 (mm-40) cc_final: 0.6542 (mp-120)
REVERT: A  580 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7541 (ptt90)
REVERT: A  871 TRP cc_start: 0.6045 (t60) cc_final: 0.5289 (t60)
REVERT: A 1094 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.7042 (mtm180)
REVERT: A 1192 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.6298 (mm-30)
REVERT: A 1203 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6680 (mt-10)
  outliers start: 30
  outliers final: 16
  residues processed: 98
  average time/residue: 0.8373
  time to fit residues: 88.4161
Evaluate side-chains
  94 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 73
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  239 MET
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  391 PHE
Chi-restraints excluded: chain A residue  557 ILE
Chi-restraints excluded: chain A residue  580 ARG
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  661 THR
Chi-restraints excluded: chain A residue  716 SER
Chi-restraints excluded: chain A residue  728 VAL
Chi-restraints excluded: chain A residue  846 TYR
Chi-restraints excluded: chain A residue  895 VAL
Chi-restraints excluded: chain A residue  917 VAL
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue 1000 ILE
Chi-restraints excluded: chain A residue 1094 ARG
Chi-restraints excluded: chain A residue 1161 LEU
Chi-restraints excluded: chain A residue 1164 THR
Chi-restraints excluded: chain A residue 1168 THR
Chi-restraints excluded: chain A residue 1192 GLU
Chi-restraints excluded: chain A residue 1203 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 75 optimal weight:    2.9990
   chunk 53 optimal weight:    0.0270
   chunk 15 optimal weight:    4.9990
   chunk 66 optimal weight:    0.8980
   chunk 58 optimal weight:    0.0980
   chunk 59 optimal weight:    0.3980
   chunk 82 optimal weight:    0.9980
   chunk 38 optimal weight:    0.0970
   chunk 39 optimal weight:    0.0870
   chunk 68 optimal weight:    0.8980
   chunk 31 optimal weight:    3.9990
   overall best weight:    0.1414

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 356 ASN
A 393 GLN
** A 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.177940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.150210 restraints weight = 8783.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.3970 rms_B_bonded: 3.02
r_work: 0.3855 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6532
moved from start:          0.1680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   6721  Z= 0.144
  Angle     :  0.548   9.682   9198  Z= 0.266
  Chirality :  0.041   0.135   1017
  Planarity :  0.004   0.044   1205
  Dihedral  :  4.390  43.244    961
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 30.37 %
    Favored  : 65.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.29), residues: 874
  helix:  0.86 (0.37), residues: 211
  sheet: -0.57 (0.39), residues: 166
  loop :  0.15 (0.29), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 658 
 HIS   0.002   0.000   HIS A 299 
 PHE   0.012   0.001   PHE A 659 
 TYR   0.022   0.001   TYR A1019 
 ARG   0.007   0.000   ARG A 786 

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 77
  time to evaluate  : 0.695 
Fit side-chains
   revert: symmetry clash
REVERT: A  239 MET cc_start: 0.5434 (OUTLIER) cc_final: 0.4955 (ppp)
REVERT: A  263 ARG cc_start: 0.6028 (ttt90) cc_final: 0.5625 (tpp80)
REVERT: A  334 SER cc_start: 0.8476 (t) cc_final: 0.7440 (p)
REVERT: A  580 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7485 (ptt90)
REVERT: A  871 TRP cc_start: 0.6047 (t60) cc_final: 0.5339 (t60)
REVERT: A 1094 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.6992 (mtm180)
REVERT: A 1192 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.6255 (mm-30)
  outliers start: 23
  outliers final: 12
  residues processed: 97
  average time/residue: 0.8358
  time to fit residues: 87.1263
Evaluate side-chains
  86 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 0.714 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 MET
Chi-restraints excluded: chain A residue  391 PHE
Chi-restraints excluded: chain A residue  393 GLN
Chi-restraints excluded: chain A residue  580 ARG
Chi-restraints excluded: chain A residue  661 THR
Chi-restraints excluded: chain A residue  716 SER
Chi-restraints excluded: chain A residue  728 VAL
Chi-restraints excluded: chain A residue  846 TYR
Chi-restraints excluded: chain A residue  888 THR
Chi-restraints excluded: chain A residue  917 VAL
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue 1094 ARG
Chi-restraints excluded: chain A residue 1161 LEU
Chi-restraints excluded: chain A residue 1165 VAL
Chi-restraints excluded: chain A residue 1168 THR
Chi-restraints excluded: chain A residue 1192 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 20 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   chunk 24 optimal weight:    6.9990
   chunk 34 optimal weight:    2.9990
   chunk 75 optimal weight:    5.9990
   chunk 69 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0170
   chunk 64 optimal weight:    0.6980
   chunk 23 optimal weight:    0.0060
   chunk 51 optimal weight:    0.4980
   chunk 87 optimal weight:    1.9990
   overall best weight:    0.3834

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 338 GLN
A 356 ASN
A 393 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.176375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.148529 restraints weight = 8939.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.3949 rms_B_bonded: 3.03
r_work: 0.3834 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6559
moved from start:          0.1722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6721  Z= 0.169
  Angle     :  0.574   9.484   9198  Z= 0.277
  Chirality :  0.041   0.135   1017
  Planarity :  0.004   0.045   1205
  Dihedral  :  4.381  41.116    961
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 30.87 %
    Favored  : 65.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.29), residues: 874
  helix:  0.87 (0.37), residues: 211
  sheet: -0.56 (0.39), residues: 166
  loop :  0.17 (0.29), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP A1005 
 HIS   0.004   0.000   HIS A 299 
 PHE   0.013   0.001   PHE A 659 
 TYR   0.017   0.001   TYR A1019 
 ARG   0.005   0.000   ARG A 786 

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 70
  time to evaluate  : 0.744 
Fit side-chains
   revert: symmetry clash
REVERT: A  239 MET cc_start: 0.5424 (OUTLIER) cc_final: 0.4923 (ppp)
REVERT: A  334 SER cc_start: 0.8632 (t) cc_final: 0.7890 (p)
REVERT: A  580 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7587 (ptt90)
REVERT: A  871 TRP cc_start: 0.6073 (t60) cc_final: 0.5349 (t60)
REVERT: A 1094 ARG cc_start: 0.7292 (OUTLIER) cc_final: 0.7053 (mtm180)
REVERT: A 1192 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.6331 (mm-30)
REVERT: A 1203 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6670 (mt-10)
  outliers start: 24
  outliers final: 15
  residues processed: 90
  average time/residue: 0.8665
  time to fit residues: 83.9958
Evaluate side-chains
  88 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 68
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  239 MET
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  391 PHE
Chi-restraints excluded: chain A residue  580 ARG
Chi-restraints excluded: chain A residue  661 THR
Chi-restraints excluded: chain A residue  716 SER
Chi-restraints excluded: chain A residue  728 VAL
Chi-restraints excluded: chain A residue  846 TYR
Chi-restraints excluded: chain A residue  888 THR
Chi-restraints excluded: chain A residue  917 VAL
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue 1000 ILE
Chi-restraints excluded: chain A residue 1092 ASP
Chi-restraints excluded: chain A residue 1094 ARG
Chi-restraints excluded: chain A residue 1161 LEU
Chi-restraints excluded: chain A residue 1165 VAL
Chi-restraints excluded: chain A residue 1168 THR
Chi-restraints excluded: chain A residue 1192 GLU
Chi-restraints excluded: chain A residue 1203 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 50 optimal weight:    0.6980
   chunk 20 optimal weight:    0.1980
   chunk 57 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9990
   chunk 76 optimal weight:    0.4980
   chunk 28 optimal weight:    3.9990
   chunk 2 optimal weight:    0.8980
   chunk 79 optimal weight:    0.0980
   chunk 51 optimal weight:    0.5980
   chunk 33 optimal weight:    0.4980
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.3780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 356 ASN
A 393 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.176042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.148027 restraints weight = 8882.355|
|-----------------------------------------------------------------------------|
r_work (start): 0.3945 rms_B_bonded: 3.01
r_work: 0.3829 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6605
moved from start:          0.1764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6721  Z= 0.168
  Angle     :  0.574   9.514   9198  Z= 0.278
  Chirality :  0.041   0.137   1017
  Planarity :  0.004   0.045   1205
  Dihedral  :  4.409  42.669    961
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 31.38 %
    Favored  : 64.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.29), residues: 874
  helix:  0.90 (0.37), residues: 210
  sheet: -0.59 (0.39), residues: 166
  loop :  0.21 (0.29), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A1005 
 HIS   0.004   0.000   HIS A 299 
 PHE   0.013   0.001   PHE A 659 
 TYR   0.019   0.001   TYR A1019 
 ARG   0.005   0.000   ARG A 786 

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 73
  time to evaluate  : 0.623 
Fit side-chains
   revert: symmetry clash
REVERT: A  239 MET cc_start: 0.5457 (OUTLIER) cc_final: 0.4891 (ppp)
REVERT: A  334 SER cc_start: 0.8535 (t) cc_final: 0.8047 (p)
REVERT: A  580 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7558 (ptt90)
REVERT: A  871 TRP cc_start: 0.6137 (t60) cc_final: 0.5419 (t60)
REVERT: A 1094 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.7063 (mtm180)
REVERT: A 1192 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.6359 (mm-30)
REVERT: A 1203 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6676 (mt-10)
  outliers start: 23
  outliers final: 16
  residues processed: 92
  average time/residue: 0.8551
  time to fit residues: 84.5304
Evaluate side-chains
  93 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 72
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  239 MET
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  391 PHE
Chi-restraints excluded: chain A residue  393 GLN
Chi-restraints excluded: chain A residue  580 ARG
Chi-restraints excluded: chain A residue  661 THR
Chi-restraints excluded: chain A residue  716 SER
Chi-restraints excluded: chain A residue  728 VAL
Chi-restraints excluded: chain A residue  846 TYR
Chi-restraints excluded: chain A residue  888 THR
Chi-restraints excluded: chain A residue  917 VAL
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue 1000 ILE
Chi-restraints excluded: chain A residue 1092 ASP
Chi-restraints excluded: chain A residue 1094 ARG
Chi-restraints excluded: chain A residue 1161 LEU
Chi-restraints excluded: chain A residue 1165 VAL
Chi-restraints excluded: chain A residue 1168 THR
Chi-restraints excluded: chain A residue 1192 GLU
Chi-restraints excluded: chain A residue 1203 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 78 optimal weight:    0.4980
   chunk 65 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 33 optimal weight:    0.2980
   chunk 51 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 66 optimal weight:    0.0170
   chunk 71 optimal weight:    0.8980
   chunk 11 optimal weight:    0.6980
   chunk 56 optimal weight:    0.7980
   overall best weight:    0.4618

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 338 GLN
A 356 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.176068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.147946 restraints weight = 9002.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.3936 rms_B_bonded: 3.03
r_work: 0.3821 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6569
moved from start:          0.1776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.196   6721  Z= 0.328
  Angle     :  1.042  59.195   9198  Z= 0.615
  Chirality :  0.043   0.393   1017
  Planarity :  0.004   0.045   1205
  Dihedral  :  4.414  42.650    961
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 31.04 %
    Favored  : 64.93 %
  Cbeta Deviations :  0.12 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.29), residues: 874
  helix:  0.91 (0.37), residues: 210
  sheet: -0.59 (0.39), residues: 166
  loop :  0.21 (0.29), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A1005 
 HIS   0.004   0.000   HIS A 299 
 PHE   0.013   0.001   PHE A 659 
 TYR   0.012   0.001   TYR A 273 
 ARG   0.007   0.000   ARG A1089 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4932.67 seconds
wall clock time: 84 minutes 44.36 seconds (5084.36 seconds total)